Question 2. The alignment results produced by the 2 tools for each of the three sets of upstream nucleotide sequences are given below. DIALIGN again seemed to produce better alignments that CLUSTALW. The alignments produced by DIALIGN for the sets are listed below.(CLSUTALW alignments are at the end). Set 1: No sequences are perfectly conserved in this alignment. Some sequences are conserved partially. The sequence ‘AAATTA’ was the best-aligned sequence. This is shown below. The prokaryotes, proteins and IDs are: Protein PID Orgnanism 1.isoleucyl-tRNA synthetase 15673845 Lactococcus lactis subsp. lactis 2.isoleucyl-tRNA synthetase 15901494 Streptococcus pneumoniae TIGR4 3.isoleucyl-tRNA synthetase 15903545 Streptococcus pneumoniae R6 4.isoleucyl-tRNA synthetase 25010601 Streptococcus agalactiae NEM316 5.isoleucyl-tRNA synthetase 22536664 Streptococcus agalactiae 2603V/R 6.isoleucyl-tRNA synthetase 16804058 Listeria monocytogenes 7.isoleucyl-tRNA synthetase 16801193 Listeria innocua 8.isoleucyl-tRNA synthetase 15615108 Bacillus halodurans 9.isoleucyl-tRNA synthetase 16078607 Bacillus subtilis Motif 1: 1 88 GCAGTAACCA ATCAAAAATg ccttc----- ---------- ---------- 2 64 AAAGTACCAT A--------- ---------- ---------- ---------- 3 65 AAAGTACCAT AGAGGAAATa tttattaTTG TTTAATTTTT Ggtgctgaag 4 72 AAATTATCAT ---------- -------TTT CAATCATT-- ---------- 5 72 AAATTATCAT ---------- -------TTT CAATCATT-- ---------- 6 21 AAATAAAAAT ---------- -------TTG TGTTTTTTTA GAGAGGGTT- 7 21 AAATAAAAAT ---------- -------TTG TGTTTTTTTA GAGAGGGTT- 8 100 ---------- ---------- ---------- ---------- ---------- 9 111 AGATCAGCCC ---------- -------TTT AGTTTCCTTg ---------- ****** Set 2: Again, No sequences are perfectly conserved in this alignment. The partially conserved sequence found by DIALIGN is shown below. The prokaryotes, proteins and IDs are: Protein PID Orgnanism 1.arginyl-tRNA synthetase 15674020 Lactococcus lactis subsp. lactis 2.Arginyl-tRNA synthetase 15903931 Streptococcus pneumoniae R6 (arginine--tRNA ligase) 3.arginyl-tRNA synthetase 15901895 Streptococcus pneumoniae TIGR4 4.arginyl-tRNA synthetase 25012094 Streptococcus agalactiae NEM316 5.arginine-tRNA ligase 18310643 Clostridium perfringens 6.Arginyl-tRNA synthetase 15894328 Clostridium acetobutylicum 7.arginine-tRNA ligase 15613397 Bacillus halodurans Motif 1: 1 44 ---------- AA-------- ---------- ----CCGA-- ATGATTAACA 2 98 CTATATTTAT AA-------- ---------- ----CCAT-- ATTATACCAA 3 110 CTATATTTAT AA-------- ---------- ----CCAT-- ATTATACCAA 4 17 TTATGCTT-- -A-------- ---------- ----CCAA-- ATTATATCAA 5 75 CGAAAGTCAT AAaagcgagt cgggatggtg ggagCCGA-- TTGgactggt 6 282 CTAAGGAG-- -G-------- ---------- ----CAAA-- ATTGT----- 7 181 TTATTTTTAT GA-------- ---------- ----TCAata ATTTTACgtt ****** Set 3: No sequences are perfectly conserved in this alignment. The partially conserved sequences were ‘AGCCGTGACT’ (found in 6 of 8 upstream sequences) and ‘AATAGA’ (4 of 8 sequences). The prokaryotes, proteins and IDs are: Protein PID Orgnanism 1.phenylalanil-tRNA synthetase alpha chain 15673911 Lactococcus lactis subsp. lactis 2.Phenylalanyl-tRNA synthetase alpha chain 15902551 Streptococcus pneumoniae R6 3.phenylalanyl-tRNA synthetase 15900489 Streptococcus pneumoniae TIGR4 4.phenylalanyl-tRNA synthetase, 22537032 Streptococcus agalactiae 2603V/R 5.Phenylalanyl-tRNA synthetase alpha chain 25010941 Streptococcus agalactiae NEM316 6.phenylalany-tRNA synthetase alpha subunit 16800253 Listeria innocua 7.phenylalanyl-tRNA synthetase alpha subunit 23099586 Oceanobacillus iheyensis 8.phenylalany-tRNA synthetase alpha subunit 16803261 Listeria monocytogenes Motif 1: 1 145 ---------- ---------- ---------- ---------- ---------- 2 157 TGAAAGACTA GTAGCCCAAG GGAAGTATAT CAGGGAGGAG AGCCGTGACT 3 238 TGAAAGACTA GTAGCCCAAG GGAAGTATAT CAGGGAGGAG AGCCGTGACT 4 69 TGTGAGACTA GTAAACCAAG GGAAGCTGCT TAGGGAGTTC AGCCGTGACT 5 69 TGTGAGACTA GTAAACCAAG GGAAGCTGCT TAGGGAGTTC AGCCGTGACT 6 159 ---------- ---------G TGAAGGTGGT CCGGTTACTA AGCCGTTATC 7 169 ---------- ---------G TGAAGGTGGT CCGGTTACTA AGCCGTTATC 8 86 ---------- ---------- ---------- ---------- ---------- ********** Motif 2: 1 129 ct-------- ---------- ----AAATTA TCTTTTAT-- ---------- 2 107 TGCAAGAATG GTAAAAATCT GATAAACTAA GTaGTAATTG AATAGGAATC 3 188 TGCAAGAATG GTAAAAATCT GATAAACTAA GTgGTAATTG AATAGAAATC 4 19 TGTTAAAGAC TGAAAAATTT GATAAAATAG TCTTTAATTG AATAGAGGTC 5 19 TGTTAAAGAC TGAAAAATTT GATAAAATAG TCTTTAATTG AATAGAGGTC 6 159 ---------- ---------- ---------- ---------- ---------- 7 169 ---------- ---------- ---------- ---------- ---------- 8 86 ---------- ---------- ---------- ---------- ---------- ******